Thursday, December 20, 2007
But at times like this, the term "missing link" likes to fly around in the popular media (but certainly not in Carl Zimmer's writing!). "Missing link" has a certain seductive quality in that it's a familiar concept and can be used to easily grab the interest of lay readership. But therein lies the problem: this does nothing to dispel the misleading notions carried with the term "missing link", and instead only perpetuates them.
As others have pointed out, I'm sure, evolution is not viewed as a chain or a ladder, and concepts that apply such linearity are definitely misleading. However, one could defend the term by nothing that, often times, a fossil might alter the grouping we make and thus "link" one group to another group -- something we didn't know before. But even if that is the case (and it rarely is), no single fossil holds a privileged place in illuminating the tree of life. We understand the importance of a fossil, such as Indohyus, because of what it shares in common (or doesn't share in common) with other fossil forms and other living taxa as well.
Indeed, these forms to which we often apply the label "missing link" do demonstrate structures and charicter combinations that are in some sense intermediate between groups as we recognise them, but that is somewhat misleading as well. For instance, Tiktaalik is widely regarded as a "fish-tetrapod intermediate". In a sense this is true, but it implies the reality of fish as distinct from tetrapods and that one animal somehow bridges this otherwise un-crossable boundary between types. Instead, we understand tetrapods as nested within the bony fishes, with the lobe-finned fishes sharing a special common grouping with them. Among these lobe-finned fishes exists a range of forms that are either more or less like tetrapods than others.
It is within this comparative context that transitions are understood. Sequences of character change are built up be recognizing the common features shared among groups in a hierarchy. It is thus a branching picture, rather than a straight chain with some missing links. The so-called "missing links" get portrayed as somehow essential to the whole story, the last piece of evidence required to prove some otherwise incomplete notion. In reality what they do is quite often to fit neatly into a picture that we already understand very well and serve instead to make the details much clearer.
In the case of Indohyus, it adds important new information in understanding the origin of whales, both from a phylogenetic perspective, but mostly from a functional and ecological perspective. It's not so much a "missing link" no longer missing, as a piece of the puzzle that helps us decide between competing solutions.
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Thursday, December 06, 2007
It's tempting to write a counter rebuttal here, but I'll just let you read the papers if you have access to them. The point is, this is how science works: we depend on other workers being willing and able to criticise our work when they think there is reason to do so. Because of this, science maintains its credibility and its integrity. A case example for your edification. Enjoy.
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Wednesday, April 18, 2007
A brief coffee break at the town of Yea. Delegates enjoy hot cross buns, given that it was Easter weekend.
The first of our stops was a site near Yea where the Silurian beds have produced the articulated remains of a single fish, Yealepis, described by Carole Burrow and Gavin Young in 1997. Yealepis looks like an acanthodian-type fish, but has no fin spines. Fancy that.
John Long holds a specimen of Yealepis and directs our attention to the Silurian beds exposed along a road cut. This photo was taken near the site where Yealepis was recovered. Sadly, the exact locality is not known.
The evening of the 9th was spent at the Mansfield Backpacker's Inn (which I recommend). We headed out to a site on a farm in the Mansfield district where some Carboniferous sand- and siltstones were cropping out in a field and along a river. Sadly, we didn't see a platypus or any snakes.
The fossils here are very rare and and the rock exposures are rather limited. However, in these beds, a number of important fossil fishes have been discovered, including early actinopterygians and some of the first-known rhizodontid material. More recently, a large and disarticulated skull and articulated fin of the rhizodontid Barameda was discovered here. It represents one of the most anatomically informative rhizodontid specimens and is to be published in the next issue of Journal of Vertebrate Paleontology. I will say no more until that time.
Conference delegates dig in to the Carboniferous sand and siltstones at Mansfield.
Beautiful vistas seen from the outcrops.
Anne Warren (La Trobe University) points out unusual sedimentary structures in the rock exposed in the creek bed. In this area, numerous spines of gyracanth fishes have been found.
The site has been well picked over, but a lot of exposed rock remains. In the relatively distant future, more great discoveries may be made here, once the rock has had more time to erode.
We visited a family of Cunningham skinks tucked between layers of Carboniferous rocks.
On the 11th, we visited a Devonian fish site atop the hills of the South Blue Range. The fossils here are also scattered and rather rare. Moreover, there are not really any articulated remains but mainly isolated head and shoulder plates from placoderm fishes. Moreover, to even find those scattered fossils, one needs to find the few restricted layers that are yielding them. However, with about two dozen conference delegates scouring the hillside, we ended up doing pretty well.
Making our way to the top of the South Blue Range
The incline was steep. Don't drop your water bottle, it would almost certainly roll to the bottom of the hill. We had to be careful not to send rocks tumbling down on the people below us! Kangaroos and wallabies were spotted darting though the forest.
Damn! A centipede absconds before I can get my macro function set!
Zhu Min (IVPP) examines some placoderm bits recovered at the top of the hill.
More fish are found. More placoderms, but a few other diverse bits are showing up too. Here, John Long (Melbourne), Robert Gess (Witwatersrand), and Daniel Goujet (Paris) zoom in on some placoderm plates.
The effects of bush fires can be seen over the region. As devastating as such events may be, the forests here dominated by eucalypts depends on long, intense fires for growth and regeneration. Without fire, eucalypts will not sprout new buds and seed germination will not occur. It also bodes well for palaeontologists in that it can clear out plant cover and reveal new rock exposures! Unfortunately, the aftermath can create hazards and one of the field trip sites at Mt. Howitt had to be cancelled.
Over the hills and through the spectacular Yarra Ranges National Forest.
We travelled next to the south coast of Victoria to a Mesozoic-aged sea cliff at a site called Flat Rocks, near Inverloch. In these cliffs dinosaurs and mammal fossils have been recovered following decades of dedicated and painstaking prospecting, quarrying, and even tunnelling. The sand- and siltstones here preserve coalified wood and tree trunks. A sharp eye is needed to spot the often similar-coloured bones in the blue-ish gray rocks.
Theropod dinosaur teeth recovered from the site.
An isolated dinosaur footprint. Rare occurrences of dinosaur footprints happen here. This one is a bit beat up, but it is believed that there are two prints, one inside the other. I only see one.
One of our guides on this part of the trip, Mike Cleeland, points out a large, fallen petrified tree.
The site is particularly special, for the researchers working there believe that it represents a polar dinosaur fauna. A number of lines of evidence have been cited to suggest this. The most important has been the geophysical evidence of permafrost. A layer of intermixed mud and siltstones showing a distinctive pattern known as cryoturbation is typical and, apparently, indicative of permanent ground freezing.
The palaeogeography of this part of Australia has been considered to have been polar in the Early Cretaceous when these beds were laid down. Thus, it seems to have been the case that these dinosaurs were living in a polar climate for at least some part of the year.
Mike again, pointing out the cryoturbation. It's difficult to see, so don't squint too hard. We couldn't get close due to the hazard of falling rock.
The field trip concluded at a second, related Mesozoic fossil site near San Remo. While we didn't find any additional fossils, I think it was easy to be distracted by the spectacular beach and gorgeous sunny day! However, this site was the provenance of what is probably the latest-occurring temnospondyl amphibian, Koolasuchus. This type of amphibian occurs very early in the fossil record, during the Carboniferous not very long after the first appearance of land-living tetrapods. However, the group persists well into the Triassic period. Koolasuchus thus represents a very late survivor of this lineage.
Mike poiting out the geology near the Koolasuchus site.
Edit: Plenty more pictures can be seen at the CAVEPS site. Including this picture of yours truly taking flight! Enjoy!
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Tuesday, March 13, 2007
(Jasper is out! It's time for a paddlin'! This post is in two sections. Recognizing the potential for it to drag on into lengthy details and scare readers away, I have chosen to put the main points up front and add a supplementary section at the end for those of you who are interested in some of the additional details of biology related to this post)
Dr. David Menton of Answers in Genesis has written the latest reaction to Tiktaalik roseae. Interestingly, the article makes almost no reference to the Tiktaalik fossils themselves, except where facts are made up.
In the article, Menton's only claims about the anatomy of Tiktaalik relate to the pelvic fins and girdles (i.e. the hips and legs) of Tiktaalik. There is no disucssion of the skull or shoulder girdle, and only tacit reference to the fin skeleton. Menton explains in relation to fishes and tetrapods that:
[t]he hind limbs [of tetrapods] in particular have a robust pelvic girdle securely attached to the vertebral column. This differs radically from that of any fish including Tiktaalik. Essentially all fish (including Tiktaalik) have small pelvic fins relative to their pectoral fins.Menton is a liar. He cannot possibly know anything about the pelvic fins of Tiktaalik. The two papers describing Tiktaalik offer absolutely no descriptions of the pelvic fin skeletons or girdle. I've seen the material first-hand and there are no such details of the pelvic fin.
I took the time to go one step further. I emailed Ted Daeschler (of Colbert Report fame) who is one of the authors of the papers to drive this point home. Here's his reply which I got this morning [emphasis added]:
Regarding Tiktaalik pelvic fins . . . no pelvic fin material has been reported. Less for him to misrepresent!I know this is like taking a whizz in the ocean, but chalk up another lie for AiG.
The article is replete with misinformation, and I will only take up a few of them here. There is a "supplement" below for those who are interested in the finer details of biology or the particularly vapid claims that Menton makes. The article has some subtle ways of using definitions as though they were arguments. For instance, Menton claims that "no fish (including Tiktaalik) has true finger or toe bones." This is a "truth by definition". Tetrapods, by definition, have digited limbs. In other words, only tetrapods have true finger or toe bones by definition. If it has fingers, it ain't a fish! Menton's claim isn't even an argument, but it sure is misleading.
Edited to add. It gets worse and I can't believe I forgot to add it. Nevermind the rhetoric, Menton (who is an anatomy professor! states: "Finally, no fish (including Tiktaalik) has true finger or toe bones. Instead, fish have slender bony fin rays, which even evolutionists concede are not homologous or related in any way to digits". Rays are not in the place of digits. Rays are dermal bone, they develop in the skin like scales and skull bones. Thus, they are in the skin and form a "sandwich" over the internal, or endochonrdral/cartilage, skeleton. Digits are part of this internal skeleton. You cannot have "rays instead of digits". You may have one and not the other, but neither takes the other's anatomical place. Coming from an anatomist, this statement demonstrates first-rate incompetence. Tiktaalik does have jointed radials, a feature which is typically only in lobe-finned fishes. These are endochondral bones. Whether or not they are homologous to digits is a question of ongoing investigation which will require more fossils and involves gene expression work in lungishes.End of edit
The real problem is not even whether or not Tiktaalik has a tetrapod-like pelvic girdle. It's that Menton's attempt to discredit the claims of the authors is based on listing the fish-like aspects of Tiktaalik and ignoring the tetrapod-like aspects. An animal that is a fish-tetrapod transitional would be expected to have some properties of a fish, no?
Menton's use of quotations is also appallingly dishonest. In a section titled "So Is Tiktaalik a Missing Link?", he quotes the News and Views article by Ahlberg and Clack and states that it concedes a point he is trying to make.
In their review article on Tiktaalik, Ahlberg and Clack (Nature 440(7085):747–749) tell us that “the concept of ‘missing links’ has a powerful grasp on the imagination: the rare transitional fossils that apparently capture the origins of major groups of organisms are uniquely evocative.” The authors concede that the whole concept of “missing links” has been loaded with “unfounded notions of evolutionary ‘progress’ and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transition.”But the whole quote reveals that Menton's own choice of word's ("missing link") is a loaded question (a particularly dishonest rhetorical trick such as asking somebody "Have you stopped beating your wife yet?").
The concept of 'missing links' has a powerful grasp on the imagination: the rare transitional fossils that apparently capture the origins of major groups of organisms are uniquely evocative. But the concept has become freighted with unfounded notions of evolutionary 'progress' and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transitions. Much of the importance of transitional fossils actually lies in how they resemble and differ from their nearest neighbours in the phylogenetic tree, and in the picture of change that emerges from this pattern.Ahlberg and Clack were saying nothing like Menton's implication.
What I don't understand is why this article had to be written by a professor of anatomy. There is no cogent discussion of anatomy that is relevant to the issue of Tiktaalik. There's a heck of a lot of really bad zoology (see the supplementary section), but not even a discussion of the anatomy of of Tiktaalik. Instead, the attack is a shameful distortion of definitions, quote mining, and outright lies. To give you an impression of what Ahlberg and Clack actually think about Tiktaalik here is the figure from their article. Compare especially the skull roofs along the left-hand side of the figure, an aspect which Menton completely ignores.
Figure caption: The lineage leading to modern tetrapods includes several fossil animals that form a morphological bridge between fishes and tetrapods. Five of the most completely known are the osteolepiform Eusthenopteron16; the transitional forms Panderichthys17 and Tiktaalik1; and the primitive tetrapods Acanthostega and Ichthyostega. The vertebral column of Panderichthys is poorly known and not shown. The skull roofs (left) show the loss of the gill cover (blue), reduction in size of the postparietal bones (green) and gradual reshaping of the skull. The transitional zone (red) bounded by Panderichthys and Tiktaalik can now be characterized in detail. These drawings are not to scale, but all animals are between 75 cm and 1.5 m in length. They are all Middle–Late Devonian in age, ranging from 385 million years (Panderichthys) to 365 million years (Acanthostega, Ichthyostega). The Devonian–Carboniferous boundary is dated to 359 million years ago18.
I suspect I know why this article was written and where these comments stem from. When Tiktaalik was first reported in Nature nearly a year prior to this writing, Answers in Genesis published a screed co-authored by Menton. In response, I called out the authors for botching Vertebrate Anatomy 101. They seem to be clarifying their mistake, but I already covered that base:
On the other hand, if they're talking about the pelvic limbs, then Menton and Looy are just blowing smoke, because there is no report on the pelvic girdle here.The problem that the creationists are facing here, and what Menton's reaction is symptomatic of, is that fossils like Tiktaalik are stunningly beautiful, articulated, their implications immediately obvious even at a glance, and information about them can be disseminated widely through the world wide web. Anybody with a computer can get high-res pictures of Tikaalik and see it for themselves. In response, big-money creationists like AiG have to go through extraordinary rhetorical acrobatics to keep fleecing the flock.
Here I outline some detailed responses to claims in Menton's article but aren't necessarily related to Tiktaalik.
Part I: Fish breathing and circulation
Menton briefly discusses a number of teleost fishes that have specialized types of air breathing: mudskippers and climbing perch. Teleosts are ray-finned fishes and to put things in creationists terms: "Evolutionists" believe that all ray-finned fishes are more closely related to than they are to tetrapods. In other words, they form a clade. Conversely, there are lobe-finned or sarcopterygian fishes which "evolutionists" believe are closer to tetrapods than they are to any other fishes. Thus, they are said to form a clade with tetrapods. (Digression: It makes sense that Tikaalik is a bona fide lobe-finned fish. If it had been a teleost, that would have been a problem.) In discssing air-breathing teleosts, Menton concludes:
none of these curious fish are considered by evolutionists to be ancestors of tetrapods—they are simply interesting and specialized fish.Isn't there a glaring omission here? Has Menton not heard of lungfishes? Lungfishes are, indeed, sarcopterygian fishes. They breathe air (hence lungfishes). In fact, not only do they breath air, but their circulatory system is connected to their lung in the same way as it is in amphibians. A review of vertebrate circulatory systems can be found here, and a particular reference to the lungfishes can be found here.
Here's a little review. Vertebrates have two main types of circulation: single and double (or undivided and divided). Fishes have the single (undivided) system, and the heart is relatively simple: it's basically a muscular series of chambers. Blood is pumped through the gills where it is oxygenated and passed through the body, collected back to a major vein (common cardinal vein) and delivered back to the heart. Repeat. In tetrapods, it gets complicated where the system is double or divided. In reptiles, birds, and mammals, the blood is first sent to the lungs where it is oxygenated, then back to the heart where it goes out to the body and back. Repeat.
Amphibians and lungfishes have a system that is somewhere in between. A pulmonary artery is linked to the lung from the systemic (or gill) arches and leads to the lung where it is oxygenated. A pulmonary vein then carries blood from the lung to the heart and it is pumped back to the body. However, the heart remains largely a simple structure like in fishes. The key difference is that the atrium, the chamber that receives the blood, is partly divided to separate the flows of oxygenated blood from the lung and deoxygenated blood from the body coming back to the heart (i.e. there is some mixing, but this is also controlled a bit). This partly divided system is lacking the air-breathing fishes he talked about. It is only known in lungfishes and amphibians.
Why was this information not important enough to be included and discussed by Menton?
Part II: Air breathing "crossopterygians"?":
It gets even more deceptive where Menton notes:
Most evolutionists look to crossopterygian fish for the ancestors of tetrapods—even though unlike many living fish, none of these fish are known to be capable of either walking or breathing out of water. [Original emphasis]Very clever. "Crossopterygian" is a dated term showing that Menton has read nothing about the study of tetrapod origins or lobe-finned fish systematics from the past 20 years. Although I have a particular affection for the term, nobody uses "crossopterygian" anymore. It's Menton's convenient use of an outdated typological term that excludes lungfishes by it's definition that is particularly misleading. The term "crossopterygian" referes to a sub-group of lobe-finned fishes that included coelacanths and "osteolepiforms", the latter including the iconic Eusthenopteron frequently seen crawling out of the water in children's dinosaur books (though few scientists think it actually did this). The term is largely discarded today because it assumes that lungfishes and tetrapods are not simply modified "crossopterygians". By using this term, Menton can safely ignore lungfishes, even though most palaeontologists (and a significant number of molecular biologists) now think lungfishes are a closer living cousin than is the only living "crossopterygian", the coelacanth Latimeria. I hesitate to comment as to whether this was done on purpose by Menton, but it is rather convenient that he should choose to dig up such an old term that specifically excludes lungfishes whilst simultaneously neglecting them in a discussion of air-breathing fishes.
However, let's accept Menton's use of "crossopterygian" for the moment. Coelacanths are the only living crossopterygians. They do not have a lung, but rather an oily swim bladder. This swim bladder has a little trachea (the tube that connects the lung to the throat) and a very small version of a vein that corresponds to the pulmonary vein.
What's even more deceptive is Menton's comment that there are no crossopterygians known to breathe air when, in fact, most things that are called "crossopterygians" are extinct. While there is one living genus of coelacanth, hundreds of other genera of "crossopterygian" are extinct. Rhizodontids, "osteolepiforms", porolepiforms, onychodonts, are all "crossopterygians" and have very distinct from coelacanths and may have anywhere from half a dozen to hundreds of sub-taxa with different adaptations and, presumably, different modes of life. Of these, it is impossible to observe air-breathing. At best, some functional and/or bone histological studies might give clues to different respiratory physiology. But, at best, conclusions about air-breathing would be inferential, and thus excluded from phylogenetic analysis (i.e. interpretations of how organisms are related to each other). That said, it is yet another truism that Menton should claim that no crossopterygians are known to breathe air.
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Tuesday, February 13, 2007
A recently published paper by Trinajstic et al. in the journal Biology Letters presents the details of muscles, blood vessels and individual neurons in an extinct type of early jawed fish, the placoderms. Unfortunately, the figures are, for the most part, less than dazzling. Nevertheless, here are some examples for your edification.
a) Shows an individual muscle fiber; b) individual neuron connecting to a muscle fibre; c) capillaries (blood vessels); d) calcium phosphate crystals that make up the preserved tissues.
One of the important discoveries in this paper helps us understand how the placoderms are related to modern fishes. Over the decades, numerous hypotheses have been offered for how all the various groups of jawed vertebrates were related to each other, particularly how the fossils fit in. Fossils, of course, give us essential clues to how evolutionary transformations have taken place, but it is first important to know how they are related to each other and modern forms. Placoderms have been proposed as the sister group of sharks and their kin, of bony vertebrates, or as the most "primitive" of the jawed vertebrates.
What some of these partially articulated placoderms show is the morphology of the actual muscle blocks of the body axis.
These will add much to the debate on how placoderms may be related to modern lineages of jawed fishes. The authors of the paper note certain similarities to lamprey in these muscle blocks, suggesting that placoderms were the most primitive jawed vertebrates. However, I'm going to leave my discussion of it there and leave it to the reader to investigate this question more fully.
Update 19/02/2007: As somebody in the comments asked: how did these tissues get preserved. Yes, of course! These days, I'm so wrapped up in phylogenetic analsysi work of my own that I totally forgot about other interesting science! Yes, how are these soft tissues actually preserved.
Well, the important thing to point out is that they've been phosphatized, just like the Doushanto embryos. No these are not "fresh meat" as Karl in the comments says. So this is this really analogous to the preserved dinosaur soft tissue, either.
The authors of the paper rely on palaeoenvironmental information about the site to infer that the conditions were in fact anoxic at the immediate site of tissue preservation. In the absence of oxygen, the calcium precipitated in the local environment would've preferentially been calcium phosphate rather than calcium carbonate (limestone). The presence of microbes on the surfaces of the cells served to concentrate the calcium phosphate precipipation in the place of the tissues. Remember, bacterial cells are much, much smaller than differentiated animal cells and so an entire colony of bacteria encasing an animal cell can effectively create a facsimilie of the original thing! However, my competence of the geochemistry involved in this type of preservation is quite limited and if you're interested in knowing more, I suggest looking into the process of soft tissue phosphatization for yourself.
Trinajstic, K. et al. (in press) Exceptional preservation of nerve and muscle tissues in Late Devonian placoderm fish and their evolutionary implications. Biology Letters. link
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Saturday, February 03, 2007
...but, perhaps I'll have to do a bit more reading. Perhaps not. I'd really like to see how my score stacks up to a lot of believers'. Zeno (score: 100%!) points out that a lot of non-believers know their bible as well or better than many believers. Granted, many non-believers are often 'de-converted' fundies who eventually emerged from their benighted state.
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Sunday, January 21, 2007
Fossil preservation can be a very selective thing. Some environments are more conducive to finding fossils than others. This week, I am in Wales where I had the oppotunity to visit some Early Devonian fossil sites (about 410 million years old) that are worked by a local amateur palaeontologist. At one of his sites, I pointed out some geological structure that explains the high quality of the material collected there, and the promise for more fossils. If you're out looking for fossils, this is where you want to look.
Take a look at the image below. It shows a sequence of sedimentary rock layers and shows a classic type of structure known as a channel form. Notice the two different rock types. The upper rock is a coarse material, with heavy bedding. It's base is tapered to the left forming what's normally called a "lense" or a "lenticular bed". Below it is a noticably different-textured rock. It's heavily cracked and broken up. It is mudstone.
Here's the same image with some guides.
In the mudstone below the massively bedded (typically coarse-grained, but not greatly in this case) is where the fossils are. This is one of the best types of sequences for finding fossils and, in large part, is where articulated fossil animals are to be found. It should be no surprise then, that this friend of mine has actually recovered quite a few articulated fossils from there. He became quite excited when I remarked that this is the ideal type of sedimentary sequence in which to find articulated fossils. So, let's hope, some exciting discoveries will come from this site.
Why do fossils preserve so well in these sequences? What are they? These deposits form in a river channel, and the image below shows quite nicely the lenticular shape of the channel.
What you can see is that there is deposition of sediments in one direction that partly causes the channel to migrate (concomitant erosion of the opposite bank is the other cause). In such settings, bodies of animals are buried very rapidly. Moreover, they are quite prone to flooding and the rapid deposition of sediments (that is often why the bedding above is massive, as it was filled in rapidly, rather than in progressive layering).
This is where the fossils are.
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